Re: [apbs-users] Occupancy of a molecule on the grid

[Davide M. <dm...@au...>]

Hello everyone,

I have solved (kind of) the problem simply copying the library
libmaloc.dylib located in the "apbs/lib" folder in the /usr/lib folder on
my Mac.  
I am still not sure why, launching the executable, apbs does not look for
the library in its "lib" folder but looks for it in the default lib folder
of the MacOS.

This also happens with the pre-compiled executable and I am not sure if
could be worth investigating this problem: why it happens and how it could
be automatically solved.

Anyway, glad that I solved and happy if someone else will find solutions
reading this post..;)

Thank you for your help.

Cheers,
Davide


>
>>Dear Prof. Nathan Baker,
>>
>>Many thanks for your prompt reply. I will have a try at the script.
>>However, before having the possibility to try it, I tried to compile and
>>install apbs from source code on a MacBook Pro (early 2011) using cmake.
>>Compilation and installation were successful but when I try to launch the
>>freshly created executable I get the following error:
>>
>>dyld: Library not loaded: libmaloc.dylib
>>  Referenced from: /Users/DMac/progs/apbs/bin/./apbs
>>  Reason: image not found
>>Trace/BPT trap: 5
>>
>>It looks like the executable is not able to load the library
>>"libmaloc.dylib" that is placed into the lib folder.
>>Running the command:
>>
>>otool -L /Users/DMac/progs/apbs/bin/apbs
>>
>>Gives the following:
>>
>>/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>>169.3.0)
>>	libmaloc.dylib (compatibility version 0.0.0, current version 0.0.0)
>>	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
>>1.2.5)
>>	/Users/DMac/progs/apbs/lib/libapbs_generic.dylib (compatibility version
>>0.0.0, current version 0.0.0)
>>	/Users/DMac/progs/apbs/lib/libapbs_pmgc.dylib (compatibility version
>>0.0.0, current version 0.0.0)
>>	/Users/DMac/progs/apbs/lib/libapbs_mg.dylib (compatibility version
>>0.0.0,
>>current version 0.0.0)
>>
>>And shows that the libmaloc.dylib is the only one that doesn't have a
>>path. 
>>Can you please help me to understand where the problem is and how I can
>>solve it? Please note that is happens exactly in the same way when I
>>download and try to launch the pre-compiled executable for MacOS.
>>
>>Thank you in advance for your kind reply.
>>
>>Cheers,
>>Davide 
>> 
>>
>>
>>On 17/01/13 3:18 PM, "Baker, Nathan" <Nat...@pn...> wrote:
>>
>>>Hi Davide --
>>>
>>>The "psize.py" script provided with APBS (tools/manip/psize.py or
>>>http://sourceforge.net/p/apbs/code/ci/9527462a39126fb6cd880924b3cc4880ec
>>>4
>>>b
>>>78a9/tree/tools/manip/psize.py) will provide some of this type of
>>>information.  Have you tried that?
>>>
>>>Thanks,
>>>
>>>__________________________________________________
>>>Nathan Baker
>>>Pacific Northwest National Laboratory
>>>Phone:  +1-509-375-3997
>>>http://nabaker.me
>>>
>>>
>>>From: Davide Mercadante
>>><dm...@au...<mailto:dm...@au...>>
>>>Date: Wednesday, January 16, 2013 5:41 PM
>>>To: APBS-USERS mailing list
>>><apb...@li...<mailto:apb...@li...
>>>t
>>>>
>>>>, APBS-USERS mailing list
>>>><apb...@go...<mailto:apb...@go...>>
>>>Subject: [apbs-users] Occupancy of a molecule on the grid
>>>
>>>Dear APBS users,
>>>
>>>i have been performing electrostatic calculations on a macromolecular
>>>complex using APBS with the aim to have an electrostatic binding energy
>>>profile along a reaction trajectory (MD frames)...
>>>
>>>In order to do this and minimize accuracies I have chosen a focusing
>>>approach with grid dimensions of 161 A^3 (cubic grid) and glen variable
>>>across three calculations (an initial one (bcfl = zero) and two
>>>subsequent focusing calculations (bcfl = focus)) in which the glen was
>>>200, 100 and 75^3 respectively.
>>>
>>>I was wondering how I could calculate, how much of the complex occupies
>>>the grid in the three different glen conditions. Is there an empirical
>>>relation that allows me to calculate how much (percentage will do) of
>>>the
>>>complex is actually occupying the grid?
>>>
>>>I would expect that decreasing glen such percentage would increase.
>>>
>>>Can you please advice me on this?
>>>
>>>Thank you very much in advance for any response.
>>>
>>>Davide
>>>
>>
>>
>
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